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  "Date": "2025-09-03",
  "Title": "Classes and Methods for \"Class Discovery\" with Microarrays or\nProteomics",
  "Authors@R": "person(given = c(\"Kevin\", \"R.\"), family = \"Coombes\",\nrole = c(\"aut\", \"cre\"), email = \"krc@silicovore.com\")",
  "Description": "Defines the classes used for \"class discovery\" problems in\nthe OOMPA project (<http://oompa.r-forge.r-project.org/>).\nClass discovery primarily consists of unsupervised clustering\nmethods with attempts to assess their statistical significance.",
  "License": "Apache License (== 2.0)",
  "LazyLoad": "yes",
  "biocViews": "Microarray, Clustering",
  "URL": "http://oompa.r-forge.r-project.org/",
  "Repository": "https://r-forge.r-universe.dev",
  "Date/Publication": "2026-05-22 18:40:06 UTC",
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  "Maintainer": "Kevin R. Coombes <krc@silicovore.com>",
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  "_realowner": "r-forge",
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      "date": "2017-07-12"
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    "aspectHeatmap",
    "BootstrapClusterTest",
    "cluster3",
    "cutHclust",
    "cutKmeans",
    "cutPam",
    "cutRepeatedKmeans",
    "distanceMatrix",
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    "hist",
    "identify",
    "image",
    "mahalanobisQC",
    "Mosaic",
    "PCanova",
    "pcc",
    "PerturbationClusterTest",
    "plot",
    "plotColoredClusters",
    "pltree",
    "predict",
    "repeatedKmeans",
    "SamplePCA",
    "screeplot",
    "summary",
    "text"
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    {
      "page": "cd06-0-aspectHeatmap",
      "title": "Heatmap with control over the aspect ratio",
      "topics": [
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    {
      "page": "cd03-1-BootstrapClusterTest-class",
      "title": "Class \"BootstrapClusterTest\"",
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        "BootstrapClusterTest",
        "BootstrapClusterTest-class",
        "summary,BootstrapClusterTest-method"
      ]
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    {
      "page": "cd02-1-cluster3",
      "title": "Cluster a Dataset Three Ways",
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        "cluster3"
      ]
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    {
      "page": "cd03-0-ClusterTest-class",
      "title": "Class \"ClusterTest\"",
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        "ClusterTest",
        "ClusterTest-class",
        "hist,ClusterTest-method",
        "image,ClusterTest-method",
        "summary,ClusterTest-method"
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    },
    {
      "page": "cd01-0-distanceMatrix",
      "title": "Distance Matrix Computation",
      "topics": [
        "distanceMatrix"
      ]
    },
    {
      "page": "cd05-1-GenePCA-class",
      "title": "Class \"GenePCA\"",
      "topics": [
        "GenePCA",
        "GenePCA-class",
        "plot,GenePCA,missing-method"
      ]
    },
    {
      "page": "cd03-2-hclust-class",
      "title": "Class \"hclust\"",
      "topics": [
        "hclust-class"
      ]
    },
    {
      "page": "cd03-3-justClusters",
      "title": "Get the List of Classes From A Clustering Algorithm",
      "topics": [
        "cutHclust",
        "cutKmeans",
        "cutPam",
        "cutRepeatedKmeans",
        "repeatedKmeans"
      ]
    },
    {
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      "title": "Using Mahalanobis Distance and PCA for Quality Control",
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        "mahalanobisQC"
      ]
    },
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      "title": "Class \"Mosaic\"",
      "topics": [
        "Mosaic",
        "Mosaic-class",
        "plot,Mosaic,missing-method",
        "pltree,Mosaic-method",
        "summary,Mosaic-method"
      ]
    },
    {
      "page": "cd08-0-PCanova-class",
      "title": "Class \"PCanova\"",
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        "PCanova",
        "PCanova-class",
        "plot,PCanova,missing-method",
        "pltree,PCanova-method",
        "summary,PCanova-method"
      ]
    },
    {
      "page": "cd04-0-PerturbationClusterTest-class",
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        "PerturbationClusterTest-class",
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      ]
    },
    {
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      "title": "Plot Dendrograms with Color-Coded Labels",
      "topics": [
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        "plotColoredClusters"
      ]
    },
    {
      "page": "cd05-0-SamplePCA-class",
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        "plot,SamplePCA,missing-method",
        "predict,SamplePCA-method",
        "SamplePCA",
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        "screeplot,SamplePCA-method",
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